This study presents the first annual estimates of net ecosystem exchange (NEE) of CO2 and net ecosystem carbon balances (NECB) of contrasting Danish agricultural peatlands. Studies were done at eight sites representing permanent grasslands (PG) and rotational (RT) arable soils cropped to barley, potato or forage grasses in three geo-regional settings. Using an advanced flux-chamber technique, NEE was derived from modelling of ecosystem respiration (ER) and gross primary production (GPP) with temperature and photosynthetically active radiation as driving variables. At PG (n = 3) and RT (n = 5) sites, NEE (mean ± standard error, SE) was 5.1 ± 0.9 and 8.6 ± 2.0 Mg C ha−1 yr−1, respectively, but with the overall lowest value observed for potato cropping (3.5 Mg C ha−1 yr−1). This was partly attributed to a short-duration vegetation period and drying of the soil especially in potato ridges. NECB, derived from NEE and C-removal in harvested biomass, was equivalent to 8.4 ± 1.0 and 11.5 ± 2.0 Mg C ha−1 for the PG and RT land-use types, respectively. Means were not significantly different, P = 0.214, and were comparable to a wider range of high-end emission factors for managed organic soils in boreal and temperate climate zones. It was stressed that evaluation of emission factors should explicitly differentiate between data representing net C balance from a soil perspective and CO2-C balance from an atmospheric perspective. Modelling of inter-annual variability in NEE for three selected sites during a 21-year meteorological period indicated a range of 18–67% (coefficients of variation). Yet, the robustness of these estimates and their importance for the derived emission factors needs to be substantiated experimentally.